tbuckley/cabot-search huggingface dataset:
Real-time guiding by deep learning during echocardiography to reduce left ventricular foreshortening and measurement variability
Authors: Sigbjorn Sabo, Hakon Neergaard Pettersen, Erik Smistad, David Pasdeloup, Stian Bergseng Stølen, Bjørnar Leangen Grenne, Lasse Lovstakken, Espen Holte, Havard Dalen
Journal:  (2023)

Abstract Aims Apical foreshortening leads to an underestimation of left ventricular (LV) volumes and an overestimation of LV ejection fraction and global longitudinal strain. Real-time guiding using deep learning (DL) during echocardiography to reduce foreshortening could improve standardization and reduce variability. We aimed to study the effect of real-time DL guiding during echocardiography on measures of LV foreshortening and inter-observer variability. Methods and results Patients (n = 88) in sinus rhythm referred for echocardiography without indication for contrast were included. All participants underwent three echocardiograms. The first two examinations were performed by sonographers, and the third by cardiologists. In Period 1, the sonographers were instructed to provide high-quality echocardiograms. In Period 2, the DL guiding was used by the second sonographer. One blinded expert measured LV length in all recordings. Tri-plane recordings by cardiologists were used as reference. Apical foreshortening was calculated at the end-diastole. Both sonographer groups significantly foreshortened the LV in Period 1 (mean foreshortening: Sonographer 1: 4 mm; Sonographer 2: 3 mm, both P &amp;lt; 0.001 vs. reference) and reduced foreshortening in Period 2 (2 and 0 mm, respectively. Period 1 vs. Period 2, P &amp;lt; 0.05). Sonographers using DL guiding did not foreshorten more than cardiologists (P ≥ 0.409). Real-time guiding did not improve intra-class correlation (ICC) [LV end-diastolic volume ICC, (95% confidence interval): DL guiding 0.87 (0.77–0.93) vs. no guiding 0.92 (0.88–0.95)]. Conclusion Real-time guiding reduced foreshortening among experienced operators and has the potential to improve image standardization. Even though the effect on inter-operator variability was minimal among experienced users, real-time guiding may improve test–retest variability among less experienced users. Clinical trial registration ClinicalTrials.gov, Identifier: NCT04580095.
Selected Articles from This Issue
Journal: Clinical Cancer Research (2023)

Highlights| August 01 2023 Selected Articles from This Issue Author & Article Information Online ISSN: 1557-3265 Print ISSN: 1078-0432 ©2023 American Association for Cancer Research2023American Association for Cancer Research Clin Cancer Res (2023) 29 (15): 2739. https://doi.org/10.1158/1078-0432.CCR-29-15-HI Related Content A commentary has been published: Trimodality Therapy Improves Disease Control in Radiation-Associated Angiosarcoma of the Breast A commentary has been published: Genomic Profiling of Radiation-Induced Sarcomas Reveals the Immunologic Characteristics and Its Response to Immune Checkpoint Blockade A commentary has been published: Antitumor Efficacy of the Novel KIT Inhibitor IDRX-42 (Formerly M4205) in Patient- and Cell Line–Derived Xenograft Models of Gastrointestinal Stromal Tumor (GIST) View more A commentary has been published: HLA Class II Loss and JAK1/2 Deficiency Coevolve in Melanoma Leading to CD4 T-cell and IFNγ Cross-Resistance View less Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record August 1 2023 Citation Selected Articles from This Issue. Clin Cancer Res 1 August 2023; 29 (15): 2739. https://doi.org/10.1158/1078-0432.CCR-29-15-HI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search During treatment, most gastrointestinal stromal tumors (GIST) will develop secondary mutations in KIT or PDGFRA inducing drug resistance, so there is an unmet need for novel therapies. De Sutter and colleagues tested the efficacy of IDRX-42, a novel specific KIT inhibitor, which showed significant antitumor activity in patient- and cell line-derived GIST xenograft models with volumetric responses, decreased mitotic activity, antiproliferative effects, and characteristic myxoid degeneration. Based on the promising results of this in vivo work, IDRX-42 is currently being investigated in a phase I first-in-human study (NCT05489237) in participants with advanced (metastatic and/or surgically unresectable) GIST. Radiation-induced sarcomas (RIS) show poor prognosis and lack effective treatment, along with showing increasing incidence globally. Hong and colleagues performed integrative analysis for genomic, transcriptomic, and immunological profile of RISs, revealing that this tumor has higher immune cell infiltration, higher PD-1/PD-L1 expression, and greater neoantigen burden than primary sarcoma. It is proposed that... You do not currently have access to this content.
Applications of multi‐omics analysis in human diseases
Authors: Chongyang Chen, Jing Wang, Donghui Pan, Xinyu Wang, Yuping Xu, Junjie Yan, Lizhen Wang, Xifei Yang, Min Yang, Gong‐Ping Liu
Journal: MedComm (2023)

Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.
Association of substance use and other psychiatric disorders with all-cause and external-cause mortality in individuals given community sentences in Sweden: a national cohort study
Authors: Denis Yukhnenko, Nigel Blackwood, Paul Lichtenstein, Seena Fazel
Journal: The Lancet Regional Health - Europe (2023)

Consistently high rates of premature mortality have been reported in individuals who receive community sentences. However, few studies have explored potential modifiable risk factors for these rates, particularly mental health. We examined the association of substance use and other psychiatric disorders with all-cause and external-cause mortality in individuals convicted of a criminal offence and given a community sentence.
Nasal IL-13 production identifies patients with late-phase allergic responses
Authors: Nicholas J. Campion, Sergio Villazala-Merino, Ryan S. Thwaites, Victoria Stanek, Helen Killick, Eleftheria Pertsinidou, Mohammed Zghaebi, Josef Toth, Renate Fröschl, Thomas Perkmann, Katharina Gangl, Sven Schneider, Robin Ristl, Ian C. Scott, Emma Suzanne Cohen, Magnus Molin, Margit Focke-Tejkl, Guenther Regelsberger, Trevor T. Hansel, Rudolf Valenta, Verena Niederberger-Leppin, Julia Eckl-Dorna
Journal: Journal of Allergy and Clinical Immunology (2023)

There is limited knowledge on how local cytokine secretion patterns after nasal allergen challenge correlate with clinical symptoms especially with regard to the "late allergic response," which occurs in approximately 40% to 50% of patients with allergy.We sought to characterize the immunologic and clinical nasal responses to birch pollen allergen challenge with a special focus on the late allergic response.In this randomized, double-blind, placebo-controlled trial, birch pollen-allergic participants were challenged with birch pollen extract (n = 20) or placebo (n = 10) on 3 consecutive days. On days 1 and 3, nasal secretions were collected at selected time points over a 24-hour time course for the measurement of 33 inflammatory mediators. Clinical responses were determined through subjective symptom scores and objective nasal airflow measurements.Provoked participants had significantly greater clinical responses and showed significant increases in tryptase and the soluble IL-33 receptor serum stimulation 2 (sST2) in nasal secretions within minutes compared with the placebo group. Eight of 20 provoked participants displayed high IL-13 levels 2 to 8 hours after allergen provocation. This group also showed significant changes in clinical parameters, with a secondary drop in nasal airflow measured by peak nasal inspiratory flow and increased symptoms of nasal obstruction, which significantly differed from IL-13 nonresponders after 6 hours.IL-13 response status correlates with clinical responses and type 2 cytokine responses in the late phase after allergen provocation.
Patient-reported outcomes in CD30-directed CAR-T cells against relapsed/refractory CD30+ lymphomas
Authors: Nicholas P Tschernia, Hillary Heiling, Allison M Deal, Catherine Cheng, Caroline Babinec, Megan Gonzalez, J Kaitlin Morrison, Christopher Dittus, Gianpietro Dotti, Anne W Beaven, Jonathan S Serody, William A Wood, Barbara Savoldo, Natalie S Grover
Journal: Journal for ImmunoTherapy of Cancer (2023)

Chimeric antigen receptor (CAR)-T cells targeting CD30 have demonstrated high response rates with durable remissions observed in a subset of patients with relapsed/refractory CD30+ hematologic malignancies, particularly classical Hodgkin lymphoma. This therapy has low rates of toxicity including cytokine release syndrome with no neurotoxicity observed in our phase 2 study. We collected patient-reported outcomes (PROs) on patients treated with CD30 directed CAR-T cells to evaluate the impact of this therapy on their symptom experience. We collected PROs including PROMIS (Patient-Reported Outcomes Measurement Information System) Global Health and Physical Function questionnaires and selected symptom questions from the NCI PRO-CTCAE in patients enrolled on our clinical trial of CD30-directed CAR-T cells at procurement, at time of CAR-T cell infusion, and at various time points post treatment. We compared PROMIS scores and overall symptom burden between pre-procurement, time of infusion, and at 4 weeks post infusion. At least one PRO measurement during the study period was found in 23 out of the 28 enrolled patients. Patient overall symptom burden, global health and mental health, and physical function were at or above baseline levels at 4 weeks post CAR-T cell infusion. In addition, PROMIS scores for patients who participated in the clinical trial were similar to the average healthy population. CD30 CAR-T cell therapy has a favorable toxicity profile with patient physical function and symptom burden recovering to at least their baseline pretreatment health by 1 month post infusion. Trial registration number: NCT02690545.
Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)
Authors: Beatriz Tavira, Teresa Iscar, Luis Manso, Ana Santaballa, Marta Gil-Martin, Yolanda García García, Margarita Romeo, Maria Iglesias, Ana de Juan Ferré, María Pilar Barretina-Ginesta, Aranzazu Manzano, Lydia Gaba, María Jesús Rubio, Carlos E. de Andrea, Antonio González-Martín
Journal: Clinical Cancer Research (2023)

Abstract Purpose: The aim of our study was to elucidate the impact of bevacizumab added to neoadjuvant chemotherapy (NACT) on the tumor immune microenvironment and correlate the changes with the clinical outcome of the patients. Experimental Design: IHC and multiplex immunofluorescence for lymphoid and myeloid lineage markers were performed in matched tumor samples from 23 patients with ovarian cancer enrolled in GEICO 1205/NOVA clinical study before NACT and at the time of interval cytoreductive surgery. Results: Our results showed that the addition of bevacizumab to NACT plays a role mainly on lymphoid populations at the stromal compartment, detecting a significant decrease of CD4+ T cells, an increase of CD8+ T cells, and an upregulation in effector/regulatory cell ratio (CD8+/CD4+FOXP3+). None of the changes observed were detected in the intra-epithelial site in any arm (NACT or NACT-bevacizumab). No differences were found in myeloid lineage (macrophage-like). The percentage of Treg populations and effector/regulatory cell ratio in the stroma were the only two variables significantly associated with progression-free survival (PFS). Conclusions: The addition of bevacizumab to NACT did not have an impact on PFS in the GEICO 1205 study. However, at the cellular level, changes in CD4+, CD8+ lymphocyte populations, and CD8+/CD4+FOXP3 ratio have been detected only at the stromal site. On the basis of our results, we hypothesize about the existence of mechanisms of resistance that could prevent the trafficking of T-effector cells into the epithelial component of the tumor as a potential explanation for the lack of efficacy of ICI in the first-line treatment of advanced epithelial ovarian cancer. See related commentary by Soberanis Pina and Oza, p. 12
Trends and cancer-specific patterns of physical activity, sleep duration, and daily sitting time among US cancer survivors, 1997-2018
Authors: Chao Cao, Alpa V Patel, Raymond Liu, Yin Cao, Christine M Friedenreich, Lin Yang
Journal: JNCI Journal of the National Cancer Institute (2023)

Abstract Background Physical activity, sufficient sleep, and limiting sedentary time may improve cancer survivorship. Methods Utilizing US nationally representative samples from the National Health Interview Survey 1997-2018 and the National Health and Nutrition Examination Survey 2007-2018, this study investigated the trends of meeting physical activity guidelines, insufficient sleep duration, and sitting time in US cancer survivors (n = 58 527) and noncancer adults (n = 640 109). Results From 1997 to 2018, the prevalence of meeting physical activity guidelines was consistently lower in cancer survivors than in noncancer adults. Among cancer survivors, the prevalence of meeting physical activity guidelines increased from 34.9% (95% confidence interval [CI] = 33.1% to 36.8%) to 46.5% (95% CI = 45.0% to 48.1%) for aerobic (≥150 minutes per week at moderate intensity or 75 minutes per week at vigorous intensity), from 13.9% (95% CI = 12.8% to 15.1%) to 23.1% (95% CI = 21.8% to 24.4%) for muscle strengthening (≥2 days per week) activities, and from 9.5% (95% CI = 8.4% to 10.7%) to 17.9% (95% CI = 16.7% to 19.1%) for both combined (all Ptrend &amp;lt; .001). From 2004 to 2018, the prevalence of insufficient sleep duration (&amp;lt;7 hours per day) increased from 28.4% (95% CI = 26.3% to 30.5%) to 30.8% (95% CI = 29.3% to 32.2%) (Ptrend = .004). Daily sitting time increased from 6.09 hours per day (95% CI = 5.71 to 6.46 hours per day) in 2007-2008 to 7.36 hours per day (95% CI = 7.05 to 7.68 hours per day) in 2013-2014 and attenuated to 6.20 hours per day (95% CI = 5.74 to 6.65 hours per day) in 2017-2018. The pattern of physical activity, sleep, and sitting time varied by sex, race and ethnicity, body mass index, cancer type, and time since cancer diagnosis. Conclusions More than half of US cancer survivors did not meet physical activity guidelines, and a large proportion had insufficient sleep duration and prolonged sitting time.
Axicabtagene Ciloleucel in Combination with the 4–1BB Agonist Utomilumab in Patients with Relapsed/Refractory Large B-Cell Lymphoma: Phase 1 Results from ZUMA-11
Authors: Michael D. Jain, David B. Miklos, Caron A. Jacobson, John M. Timmerman, Jennifer Sun, Jenny Nater, Xiang Fang, Ankit Patel, Madison Davis, Darren Heeke, Tan Trinh, Mike Mattie, Frank Neumann, Jenny J. Kim, Christina To, Simone Filosto, Ran Reshef
Journal: Clinical Cancer Research (2023)

Chimeric antigen receptor (CAR) T-cell therapies have shown clinical benefit for patients with relapsed/refractory (R/R) large B-cell lymphoma (LBCL), yet approximately 60% of patients do not respond or eventually relapse. We investigated the safety and feasibility of the CD19-directed CAR T-cell therapy axicabtagene ciloleucel (axi-cel) in combination with the 4-1BB agonist antibody utomilumab as an approach to improve efficacy of CAR T-cell therapy.In phase 1 of the single-arm ZUMA-11 trial, patients with R/R LBCL received a single axi-cel infusion (target dose, 2 × 106 cells/kg) plus utomilumab 10 to 200 mg intravenously every 4 weeks for up to 6 months in a dose-escalation design. The primary endpoint was incidence of dose-limiting toxicities (DLT) with utomilumab. Key secondary endpoints were safety, antitumor activity, pharmacokinetics, and pharmacodynamics.No DLTs were observed among patients treated with axi-cel and utomilumab (n = 12). Grade ≥3 adverse events occurred in 10 patients (83%); none were Grade ≥3 cytokine release syndrome or neurologic events. The objective response rate was 75% and seven patients (58%) had a complete response. Peak CAR T-cell levels increased in a utomilumab dose-dependent manner up to 100 mg. Patients who received utomilumab 100 mg had persistently increased CAR T cells on days 57 to 168 compared with other dose levels. Utomilumab was associated with dose-dependent increases in IL2, IFNγ, and IL10.Utomilumab-mediated 4-1BB agonism combined with axi-cel therapy had a manageable safety profile. Dual 4-1BB and CD28 costimulation is a feasible therapeutic approach that may enhance CAR T-cell expansion in patients with LBCL.
Retraction Notice to: Neurotrophin 3 Transduction Augments Remyelinating and Immunomodulatory Capacity of Neural Stem Cells
Authors: Jingxian Yang, Yaping Yan, Yang Xia, Tingguo Kang, Xing Li, Bogoljub Ciric, Hui Xu, Abdolmohamad Rostami, Guang-Xian Zhang
Journal: Molecular Therapy (2023)

(Molecular Therapy 22, 440–450; February 2014) This article has been retracted at the request of the editor-in-chief. A third party communicated concerns of image duplication to the editorial office. Concerns were also posted to a PubPeer thread: https://pubpeer.com/publications/00EF64ADD1F5065A29DFEB5962C3F7. Similarities were found between images in this article and articles in Acta Neuropathologica (Yang et al., 2012, Acta Neuropathol. 12, 491-503, https://doi.org/10.1007/s00401-012-0989-1), The American Journal of Pathology (Yang et al., 2010, Am. J. Pathol. 177, 1989-2001, https://doi.org/10.2353/ajpath.2010.091203), and the European Journal of Pharmacology (Zhang et al., 2012, Eur. J. Pharmacol. 697, 32-39, https://doi.org/10.1016/j.ejphar.2012.10.008). Similarities were also found between two images within this article. Image analysis performed by the editorial office confirmed the findings of image reuse in Figures 2A, 5B, 7A, and 8A of the Molecular Therapy article. This reuse (and in part misrepresentation) of data without appropriate attribution represents a severe abuse of the scientific publishing system. The email from the editorial office declaring the retraction was undeliverable to the following authors: Yaping Yan, Tingguo Kang, and Hui Xu. RETRACTED: Neurotrophin 3 Transduction Augments Remyelinating and Immunomodulatory Capacity of Neural Stem CellsYang et al.Molecular TherapyFebruary, 2014In BriefThis article has been retracted: please see Elsevier Policy on Article Withdrawal ( http://www.elsevier.com/locate/withdrawalpolicy ). Full-Text PDF Open Archive
ICGC ARGO precision medicine: genomic profiling-informed prediction of immunotherapy response in two patients with metastatic head and neck squamous cell carcinoma
Authors: Riccardo Nocini, Luca Tondulli, Consuelo D’Ambrosio, Claudio Luchini, Andrew V Biankin, Raffaella Casolino, Aldo Scarpa, Michele Milella, Rita T Lawlor, Andrew V Biankin, Lincoln D Stein, Keunchil Park, Rita T Lawlor, Amber L Johns, Jan O Korbel, Nik Zeps, Mark A Rubin, Marco A Marra, Olivier Elemento, Steven Gallinger, David Tuveson, Lorenz Trumper, Raphael Koch, Aldo Scarpa, Paul Brennan, Christian Pilarsky, Sergey Nikolaev, Sun-Soo Yoon, Eun Sook Lee, Tatsuhiro Shibata, Xiaojian Wu, Jianmin Wu, Qimin Zhan, Wai Poon, Takayuki Yoshino, Khawla S. Al-Kuraya, Rosalind Eeles, Rebecca Fitzgerald, Carlos Caldas, Jean Abraham, David K Chang
Journal: The Lancet Oncology (2023)
Multiscale morphological analysis of bone microarchitecture around Mg-10Gd implants
Authors: Sandra Sefa, Jonathan Espiritu, Hanna Ćwieka, Imke Greving, Silja Flenner, Olga Will, Susanne Beuer, D.C Florian Wieland, Regine Willumeit-Römer, Berit Zeller-Plumhoff
Journal: Bioactive Materials (2023)

The utilization of biodegradable magnesium (Mg)-based implants for restoration of bone function following trauma represents a transformative approach in orthopaedic application. One such alloy, magnesium-10 weight percent gadolinium (Mg-10Gd), has been specifically developed to address the rapid degradation of Mg while enhancing its mechanical properties to promote bone healing. Previous studies have demonstrated that Mg-10Gd exhibits favorable osseointegration; however, it exhibits distinct ultrastructural adaptation in comparison to conventional implants like titanium (Ti). A crucial aspect that remains unexplored is the impact of Mg-10Gd degradation on the bone microarchitecture. To address this, we employed hierarchical three-dimensional imaging using synchrotron radiation in conjunction with image-based finite element modelling. By using the methods outlined, the vascular porosity, lacunar porosity and the lacunar-canaliculi network (LCN) morphology of bone around Mg-10Gd in comparison to Ti in a rat model from 4 weeks to 20 weeks post-implantation was investigated. Our investigation revealed that within our observation period, the degradation of Mg-10Gd implants was associated with significantly lower (p < 0.05) lacunar density in the surrounding bone, compared to Ti. Remarkably, the LCN morphology and the fluid flow analysis did not significantly differ for both implant types. In summary, a more pronounced lower lacunae distribution rather than their morphological changes was detected in the surrounding bone upon the degradation of Mg-10Gd implants. This implies potential disparities in bone remodelling rates when compared to Ti implants. Our findings shed light on the intricate relationship between Mg-10Gd degradation and bone microarchitecture, contributing to a deeper understanding of the implications for successful osseointegration.